projects:workgroups:kb-wg
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projects:workgroups:kb-wg [2015/01/14 18:07] rkboyce [Knowledgebase Workgroup] |
projects:workgroups:kb-wg [2018/09/18 13:14] (current) ericavoss [Meetings (Telecon Info)] |
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| - | ====== Knowledgebase Workgroup ====== | + | ====== Pharmacovigilance evidence investigation Workgroup ====== |
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| - | **Objective:** The objective of this workgroup (WG) is to establish an open-source standardized knowledge base for the effects of medical products and an efficient procedure for maintaining and expanding it. For a complete overview, please see the paper [[http://www.ncbi.nlm.nih.gov/pubmed/24985530|Bridging islands of information to establish an integrated knowledge base of drugs and health outcomes of interest]]. The WG's first contribution to OHDSI will be LAERTES (Largescale Adverse Effects Related to Treatment Evidence Standardization) -- a system that integrates numerous sources of evidence useful for investigating the association of drugs and health into a single system. The system will extend the OHDSI Standard Vocabulary and provide for summary and drill down evidence review use cases. The first release of LAERTES is schedule for April 2015 | + | **Objective:** The objective of this workgroup (WG) is to establish an open-source standardized knowledge base for the effects of medical products and an efficient procedure for maintaining and expanding it. For a complete overview, please see the paper [[http://www.ncbi.nlm.nih.gov/pubmed/24985530|Bridging islands of information to establish an integrated knowledge base of drugs and health outcomes of interest]]. In 2015/16 the WG contributed LAERTES (Largescale Adverse Effects Related to Treatment Evidence Standardization) -- a system that integrates several sources of evidence investigating the association of drugs and health into a single system. The first staging release of LAERTES occurred last year and is reported in https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0115-3. |
| - | **Project Lead:** [[http://ohdsi.org/who-we-are/collaborators/richard-d-boyce-2/|Richard D. Boyce, PhD]] | + | One of the primary use cases for the WG has been the creation of negative controls. Members of the WG published a paper reporting on the accuracy of automated negative control generation using machine learning and the merged evidence base: http://dx.doi.org/10.1016/j.jbi.2016.12.005 |
| - | **Project Co-Lead:** [[http://ohdsi.org/who-we-are/collaborators/1045-2/|Patrick Ryan, PhD]] | + | The current efforts of the WG are focused on improving the process of creating and maintaining the merged evidence base, providing better support in OHDSI tools for negative control generation, and developing user friendly methods for using the merged evidence base to investigate pharmacovigilance signals. Other use cases are also being discussed. The new merged evidence base is called the Common Evidence Model and is accessible by requesting data from the project leads. The WG plans to make the data accessible from the OHDSI Web API by April 2018 (see https://goo.gl/1m6NcB). |
| - | **Members:** | + | **Project Lead:** [[http://ohdsi.org/who-we-are/collaborators/erica-voss/|Erica Voss, MPH]] |
| - | See [[kb-wg#internal|Members List]] | + | **Project Co-Lead:** [[http://ohdsi.org/who-we-are/collaborators/richard-d-boyce-2/|Richard D. Boyce, PhD]] |
| + | |||
| + | |||
| + | **Members:** | ||
| **Start Date:** 6/10/2014 | **Start Date:** 6/10/2014 | ||
| - | **Repository:** [[https://github.com/OHDSI/KnowledgeBase]] | + | **Repository:** [[https://github.com/OHDSI/CommonEvidenceModel]] |
| - | **WG Minutes:** [[https://docs.google.com/document/d/1T3TlmtkCL0BCNMJAUY76h4EV2mapEMAclaRFgmY_zzE/edit?usp=drive_web|Knowledge Base WG Minutes]] | + | **WG Minutes:** [[https://docs.google.com/document/d/1T3TlmtkCL0BCNMJAUY76h4EV2mapEMAclaRFgmY_zzE/edit?usp=drive_web|WG Minutes]] |
| - | **WG Agendas:** [[http://forums.ohdsi.org/t/laertes-team-meeting-agenda/172|Knowledge Base WG Agendas]] | + | **WG Agendas:** [[http://forums.ohdsi.org/t/laertes-team-meeting-agenda/172| WG Agendas]] |
| - | </WRAP> | + | **Publications:** |
| + | E.A. Voss, R.D. Boyce, P.B. Ryan, J. van der Lei, P.R. Rijnbeek, M.J. Schuemie, Accuracy of an Automated Knowledge Base for Identifying Drug Adverse Reactions, Journal of Biomedical Informatics, Available online 16 December 2016, ISSN 1532-0464, http://dx.doi.org/10.1016/j.jbi.2016.12.005. | ||
| - | ==== Meetings ==== | + | Boyce, RD., Voss, E., Huser, V., Evans, L., Reich, C., Duke, JD., Tatonetti, NP., Lorberbaum, T., Dumontier, M., Hauben, M., Wallberg, M., Peng, L., Dempster, S., He, O., Sena, A., Koutkias, V., Natsiavas, P., Ryan, P. (Knowledge Base workgroup of the Observational Health Data Sciences and Informatics (OHDSI) collaborative). Large-scale adverse effects related to treatment evidence standardization (LAERTES): an open scalable system for linking pharmacovigilance evidence sources with clinical data. J Biomed Semantics. 2017 Mar 7;8(1):11. doi: 10.1186/s13326-017-0115-3. Available at: https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0115-3. PubMed PMID: 28270198; PubMed Central PMCID: PMC5341176. |
| - | Schedule: Every other Wednesday at 12 Eastern starting from March 12th | + | Boyce. RD., Ryan. PB., Noren. N., et al., Bridging islands of information to establish an integrated knowledge base of drugs and health outcomes of interest. Drug Safety. 2014. Volume 37, Issue 8 (2014), Page 557-567. DOI: 10.1007/s40264-014-0189-0, PubMed PMID: 24985530. PMCID: PMC4134480. http://link.springer.com/article/10.1007%2Fs40264-014-0189-0 |
| - | Please join my meeting. | + | |
| - | https://global.gotomeeting.com/join/530277469 | + | |
| - | You can call in for audio: | ||
| - | Dial +1 (646) 749-3122 | ||
| - | Access Code: 530-277-469 | ||
| - | === Minutes and Agendas === | ||
| - | **WG Minutes:** [[https://docs.google.com/document/d/1T3TlmtkCL0BCNMJAUY76h4EV2mapEMAclaRFgmY_zzE/edit?usp=drive_web|Knowledge Base WG Minutes]] | + | </WRAP> |
| - | **WG Agendas:** [[https://docs.google.com/document/d/1AZF_nSIY4bwT_bBFPpdDObRzAUVW--Ko4S5HLJ63_y8/edit?usp=drive_web|Knowledge Base WG Agendas]] | + | ==== Meetings (Telecon Info) ==== |
| + | Schedule: | ||
| + | | ||
| + | - All team call once per month on the 4th Wednesday of each month at 9-10 Eastern. | ||
| + | - Touch point call on the 2nd Wednesday of each month 9-10 Eastern | ||
| - | === Discussions === | ||
| - | [[http://forums.ohdsi.org/t/laertes-api/128|Laertes API]] | + | Please join the [[https://meet.lync.com/jnj-its/evoss3/Q7P48H1D|Skype Meeting]] |
| - | [[http://forums.ohdsi.org/t/laertes-update-of-the-pharmacovigilance-signals/173/1|update of the pharmacovigilance signals]] | + | Trouble Joining? [[https://meet.lync.com/jnj-its/evoss3/Q7P48H1D?sl=1|Try Skype Web App]] |
| - | [[http://forums.ohdsi.org/t/laertes-pre-load-queries-hoi-from-x-to-snomed-rxnorm-bd-to-cd/180|LAERTES: pre-load queries - hoi from X to snomed, rxnorm BD to CD]] | + | Toll number: +1 (908) 316-2436,,89194944# (Dial-in Number) |
| + | [[https://dialin.lync.com/6071d915-71cb-44a6-ae05-d1830c6bbb14?id=89194944|Find a Local Number]] | ||
| - | [[http://forums.ohdsi.org/t/laertes-getting-the-pivot-correct-rolling-up-from-clinical-drug-to-ingredient/181|LAERTES: getting the pivot correct - ‘rolling up’ from clinical drug to ingredient]] | ||
| - | === GitHub Issues === | + | HOW TO JOIN SKYPE MEETING AUDIO |
| - | {{ghissues OHDSI/KnowledgeBase state:open}} | + | 1. "Use Skype for Business (full audio and video experience)" Select ONLY if you are using a USB connected Audio Device and have a good network connection (DO NOT SELECT THIS OPTION IF YOU ARE DIALING IN FROM A PHONE) |
| - | === Members List === | + | 2. "Call Me at" Select if you have a phone that can be directly dialed (not supported in all countries). |
| - | - Abraham G. Hartzema, PhD, University of Florida, Gainesville, FL | + | 3."Don't join audio" Select if you will be dialing into the meeting from your phone. |
| - | - Christian Reich, MD, PhD, AstraZeneca, Waltham MA | + | IMPORTANT NOTICE: Please note that Skype For Business Meetings allow the audio and other information sent during the session to be recorded, which may be discoverable in a legal matter. By joining this session, you automatically consent to such recordings. If you do not consent to being recorded, discuss your concerns with the host or do not join the meeting. |
| - | - Christophe Lambert, PhD, University of New Mexico, Albuquerque, NM | ||
| - | - Erica A. Voss, MPH, Janssen Research and Development, Titusville, PA | + | === Discussions === |
| - | - Gianluca Trifirò, PhD, University of Messina, Messina, Italy & Erasmus University Medical Center, Rotterdam, Netherlands | + | Search for "LAERTES" on [[http://forums.ohdsi.org/]] |
| - | - J. Marc Overhage, MD, PhD, Siemens Healthcare, Malvern, PA | + | === GitHub Issues === |
| - | - Jon Duke, MD, Regenstrief Institute, Indianapolis IN | + | [[https://github.com/OHDSI/CommonEvidenceModel/issues]] |
| - | - Johan Ellenius, PhD, Uppsala Monitoring Centre, Uppsala, Sweden | ||
| - | - Lee Evans, LTS Computing LLC, Exton, PA | + | === Active members List (add or delete your name if you see an omission or error) === |
| - | - Majid Rastegar-Mojarad, MS, Mayo Clinic, Rochester, MN | + | Erica A. Voss, Janssen Research & Development, LLC, Titusville, NJ, EVoss3@its.jnj.com |
| - | - Mark Khayter, BS, Ephir, Boston, MA | + | Richard D. Boyce, University of Pittsburgh, Pittsburgh, PA, rdb20@pitt.edu |
| - | - Martijn J. Schuemie, PhD, Janssen Research and Development, Titusville, PA | + | Lee Evans, LTS Computing LLC, West Chester, PA, levans@ltscomputingllc.com |
| - | - Michel Dumontier, PhD, Stanford University, Stanford, CA | + | Anthony G. Sena, Janssen Research & Development, LLC, Titusville, NJ, asena5@its.jnj.com |
| - | - Nicholas P. Tatonetti, PhD, Columbia University, New York, NY | + | Vassilis Koutkias, Institute of Applied Biosciences, Center for Research & Technology Hellas, Thermi, Thessaloniki, Greece, vkoutkias@certh.gr |
| - | - Niklas Noren, PhD, Uppsala Monitoring Centre, Uppsala, Sweden | + | Pantelis Natsiavas, Institute of Applied Biosciences, Center for Research & Technology Hellas, Thermi, Thessaloniki, Greece, pnatsiavas@certh.gr |
| - | - Rave Harpaz, PhD, Stanford University, Palo Alto, CA | + | Manfred Hauben, MD. MPH, Pfizer Inc, New York University Medical Center, New York, NY, manfred.hauben@pfizer.com |
| - | - Vojtech Huser, MD PhD, National Institutes of Health, Bethesda, MD | + | Patrick B. Ryan, Janssen Research & Development, LLC, Titusville, NJ, ryan@ohdsi.org |
projects/workgroups/kb-wg.1421258844.txt.gz · Last modified: 2015/01/14 18:07 by rkboyce
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